Sclerotinia stem rot

Sclerotinia stem rot is one of the most economically significant canola diseases in Canada. This disease, caused by the fungus Sclerotinia sclerotiorum, is heavily influenced by environmental conditions leading up to and during the flowering period of canola, which can make predicting outbreaks difficult. Control of this disease can be achieved with risk assessment tools, fungicides, and partial resistance available in some canola cultivars.

Important tips for best management

Sclerotinia risk assessment tool (accessible from the Canola Calculator)
Use the Sclerotinia Risk Assessment Tool to help with decisions.
  • Sclerotinia stem rot is a major disease in canola most years.
    • In addition to canola, other crops can be hosts for this disease, including mustard, soybeans, sunflowers, pulses (ex. dry beans, field peas, lentils), potatoes and other vegetable crops.
    • Several broadleaf weeds are also hosts and can maintain the fungus in the soil even in non-host crop years (e.g. stinkweed, sow thistles, Canada thistle, wild mustard, redroot pigweed, knapweeds, dandelions and lambs quarters).
  • Use the sclerotinia stem rot risk assessment tool or checklist to determine if there is risk of this disease developing and if a fungicide application is warranted.
    • Risk forecasting services, like petal tests and weather models, are not yet comprehensive, but when used with checklist provide better risk predictability.
  • Sclerotinia fungicides are the best form of control when there is a high risk of disease development. Be sure to rotate fungicide groups.
  • Use moderately sclerotinia resistant or tolerant cultivars to reduce risk, remembering these are currently not as effective as fungicides.
  • Crop rotation (with non-host crops like cereals and grasses) can reduce sclerotinia stem rot in subsequent years.
  • Factors impacting a microclimate that is conducive for the development of sclerotinia stem rot can be further reduced by:
    • Using canola cultivars with low lodging scores.
    • Using row spacing that is wider (but still able to support optimal weed control) or the lower end of recommended plant densities (ex. five or six plants per square foot).
    • Avoid using more than recommended fertility rates to prevent excessive canola biomass
    • If irrigation is available, reduce water at critical sclerotinia infection timing.

About sclerotinia stem rot

Overview | What causes sclerotinia?

The fungus Sclerotinia sclerotiorum, which occurs in all the canola growing areas of Canada, causes sclerotinia stem rot of canola. Sclerotinia stem rot, or white mould as it is sometimes called, is the most destructive canola disease in Canada. The severity of sclerotinia stem rot is variable from year-to-year, region-to-region and even from field-to-field. Sclerotinia stem rot has become more serious as canola production has increased, likely due to a combination of more acres of canola in rotations and management practices that contribute to high yielding crop which produce dense canopies that have a more conducive microclimate for disease development. Wet weather has also favoured disease development in recent years1.

In 2016, sclerotinia stem rot was widespread in canola across much of Western Canada, with over 90 per cent of fields surveyed showing symptoms of infection (disease prevalence). In the Prairie provinces, the average disease incidence of fields surveyed was between 14 per cent and 30 per cent2,3,4. This incidence of disease (in 2016) would roughly equate to seven to 15 per cent yield loss. In 2019, the disease prevalence was lower ranging from 25 to 79 per cent, and the incidence ranged from five to 12 per cent.

Plants are infected with sclerotinia stem rot when the canola crop is flowering. Variation in the disease incidence and severity among fields not treated with fungicide is due to:

Sclerotinia stem rot lesion starts on canola stem
A sclerotinia stem rot lesion starts on a canola stem
  • rainfall/humidity/leaf wetness
  • soil moisture
  • crop density
  • crop canopy/plant architecture
  • crop height and vigour
  • severity of lodging
  • genetic tolerance/resistance of some varieties
  • quantity of infectious spores (ascospores)
  • timing of sclerotia germination

With the right combination of spore load, crop density and moisture conditions, severe infections can develop almost anywhere canola is grown in Canada. Even after plants are infected, the severity of sclerotinia stem rot symptoms and the resulting effect on yield will vary according to where plants are infected, crop density, lodging potential and especially the crop stage at the time of infection. Infections of the lower main stem or branch tissue initiated soon after early bloom will result in more severe symptoms.

Yield losses vary based on the reduction of seed filling per infected plant, the amount of pre-harvest shattering (causing seed loss), and the percentage of infected plants in a crop. In general, when conditions for the disease are favourable and infections are initiated during early flowering, yield reduction per infected plant can equal 50 per cent or more. Yield losses can also be attributed to fungal growth within stems and resulting lodging, which leads to some or all of the following:

  • smaller and fewer seeds
  • premature ripening
  • shattered pods
  • loss of smaller, shrunken seeds during combining

Sclerotinia sclerotiorum is virulent on over 400 other plant species, including broadleaf crops such as canola, mustard, sunflowers, beans, lentils, peas and as well as most broadleaf weeds, such as chickweed, stinkweed, hemp-nettle, thistles, shepherd’s purse, narrow-leafed hawk’s-beard, false ragweed, wild mustard among others.

Of all the canola diseases in Canada, sclerotinia stem rot is perhaps the most dramatically affected by environmental conditions. Due to the abundance of host plants, the likelihood of S. sclerotiorum being present is high. Most canola cultivars are highly susceptible to this disease. But the variability of environmental conditions (which makes it hard to predict when the disease will be an issue and control will be needed) may have the largest impact on the development of a severe infection in a field.

Disease cycle for sclerotinia stem rot

The stem rot fungus overwinters as sclerotia in the soil, in stubble at the soil surface and mixed with seed. Sclerotia can remain viable in the field for five years or more. The amount of sclerotia in the soil will largely reflect (be impacted by) the crop rotations used. The amount of sclerotia will increase under short canola rotations, when susceptible pulse or forage crops are grown in rotation or where significant broadleaf weed populations occur (especially in wetter regions of the Prairies). Areas with low rainfall are likely not conducive for the production of sclerotia and the development of the disease. Each year some sclerotia will germinate when conditions are suitable but others will remain dormant. Germination produces either mycelium, which may infect plants, especially root tissues in direct contact with sclerotia, or spore-producing apothecia.

Nearly all infections in canola result from microscopic airborne spores (called ascospores) produced by apothecia at the soil surface. However, for sclerotia to germinate and produce apothecia, they require prolonged moist soil conditions (at least 10 days above the wilting point) and moderate temperatures of 15 to 25 degrees Celsius. Normally such conditions do not occur until the crop canopy closes (typically at the late rosette stage) and permanently shades the soil surface. If the crop canopy closure coincides with a 10-day period of prolonged moist soil conditions, (which is required for sclerotia to germinate and produce apothecia) apothecia may appear as the crop starts flowering. Only sclerotia in the top few centimetres of soil will produce functional apothecia, since the apothecial stalks are rarely longer than five centimetres (two inches). Deeply buried sclerotia will not produce apothecia but can remain dormant. If brought near the surface by cultivation, they may germinate.

A single sclerotium can produce up to 15 apothecia, either at one time or over a period of weeks. Apothecia only grow from sclerotia and not from any plant tissue or residue in the soil. Occasionally apothecia can emerge from sclerotia inside plant tissue trapped within undecomposed stubble.

In Western Canada, apothecia normally begin to appear in June, but most develop during flowering. Apothecia can continue to develop until late September but the critical period for them to cause damaging infections to crops is from early to full bloom. Plant infections rarely develop before the mid-flowering stage and apothecia rarely appear in fields before plants are at the bud stage.

Spore-producing apothecia
Spore-producing apothecia

Apothecia are typically five to 15 millimetres in diameter. The upper end of this range is about the size of a small fingernail or slightly smaller than a dime. Apothecia produce millions of ascospores that are released into moving air currents. Even the lightest breeze easily carries the ascospores across a field or into adjacent fields, possibly as far as several kilometres away. Honeybees can also carry ascospores.

Ascospores normally cannot infect the leaves and stems directly, they must first grow in dead petals or other organic material adhering to leaves and stems. The petals provide the food source necessary for the spores to germinate and produce the hyphae that grow and eventually penetrate the plant. Moist conditions from rainfall or heavy dew, which may keep leaves and stems wet for two to three days, are also necessary for infection. Radiation, relative humidity and temperature influence ascospore survival.

Ascospores are fairly short-lived and only remain viable for up to four to five days. Research has found that the average ascospore survival was up to 50 per cent after two days and up to one per cent after three days of field exposure. Other factors such as exposure to radiation, higher temperatures (greater than 25 degrees Celsius) and high relative humidity (greater than 35 per cent) can result in more rapid loss of ascospore viability after one to two days on canola petals. The combination of ascospores being released and deposited on petals along with the crop coming into full bloom creates the highest risk for infection, depending on weather and environmental factors5, (Turkington, T.K., Morrall, R.A.A. and Rude, S.V. 1991. Use of Petal Infestation to Forecast Sclerotinia Stem Rot of Canola: The impact of diurnal and weather-related inoculum fluctuations. Canadian Journal of Plant Pathology. 13(4): 347-355.)),6,7.

Sclerotinia stem lesion
Sclerotinia stem lesion

Sites of initial infection become lesions on the plant, which can grow to become quite large. When lesions develop on leaves and leaf axils or bases, these lesions can spread down into the stem, invading the healthy stem tissue. A dense canopy provides higher humidity and more favourable conditions for disease development.

In some cultivars, heavy stands can lodge, and sclerotinia stem rot will spread from plant-to-plant by direct contact, especially if wet weather delays swathing or straight combining. Spread will also occur in wet newly-cut swaths. The fungus eventually forms new sclerotia in diseased plants that are returned to the soil at harvest, completing the disease cycle.

Influence of environment

Rainfall and soil moisture are necessary for sclerotia germination, spore production, and spore germination and growth. Frequently water from heavy dews dripping off the plant is enough moisture for sclerotia germination. Ideal canola growing weather is also ideal for sclerotinia stem rot.

Lesion development is favoured by humid conditions and temperatures between 20 and 25 degrees Celsius. Dry, warm conditions will impede or stop infection and lesion development, but established lesions may resume growth when favourable conditions return.


Symptoms of sclerotinia stem rot

Sclerotia bodies in a sclerotinia-infected canola stem

Sclerotinia stem rot develops late in the season, with the first visual symptoms appearing by the end of flowering. Two to three weeks after infection, soft watery lesions or areas of very light brown discolouration become obvious on the leaves, main stems and branches. Lesions expand, become greyish white, and may have faint concentric markings. Plants with girdled stems wilt, ripen prematurely and become conspicuously straw-coloured in a crop that is otherwise still green.

The stems of infected plants eventually bleach, taking on a whitish appearance and infected tissues tend to shred and shatter easily. Infected plants may produce fewer pods per plant, fewer seeds per pod or small, shrivelled seeds that blow out the back of the combine. The extent of damage depends on whether the main stems or branches are infected and at what stage during flowering infection occurs. Severely infected crops frequently lodge, are difficult to swath and shatter during swathing.

When the bleached stems of diseased plants are split open, a white mouldy growth and sclerotia are visible. Sclerotia vary in size and shape. They may be small and round like a canola seed or up to two centimetres (0.8 inch) long and cylindrical, ovoid or irregular in shape. Under moist conditions, sclerotia and the white mouldy growth may also occur on the surface of infected areas of the plant. At harvest the sclerotia are either threshed out with the seed or left in the field.

Sclerotinia management | How do you manage sclerotinia?

Sclerotinia spray decision


Fungicides are the most effective management tool to control sclerotinia stem rot in canola when the risk of infection is high. Where required, the use of fungicides not only protects (remaining) yield but also reduces dockage caused by sclerotia contamination and small, shrivelled seed. Since the cost of spraying a fungicide is high and sclerotinia disease incidence varies greatly among years, regions, and fields, systematic spraying is not profitable. By estimating the risk of infection, severe yield losses and unnecessary fungicide applications can be avoided1.

There are several fungicides registered for sclerotinia stem rot control in canola (provincial crop protection guide should always be consulted for an up-to-date list of registered products). Most fungicides recommend timing application to cover the maximum number of canola petals with fungicide at the early stage of the flowering period. Some of these products are registered for a split application, which has the advantage of providing longer protection if the bloom period is extended due to cool, wet conditions or uneven maturity due to staggered emergence or excessive branching from low plant populations. There are also biological products available, which may require differing methods and timings of application.

Table 1. Sclerotinia stem rot fungicides for canola in Canada

Source: Guide to Field Crop Protection 2024 (Manitoba Edition)

Sclerotinia fungicide timing

Fungicide timing

If planning to use a fungicide for sclerotinia control, the optimal time to spray must be decided. For most fungicides, the recommended window for application falls between 20 and 50 per cent bloom, with optimum timing typically around 30 per cent bloom. To assess the bloom stage, sample several plants over the field and count the number of open flowers. One method is to identify the main stem, remove the secondary branches, and count only the open flowers on the main stem. Generally, it takes a crop two to four days to move from first flower to 10 per cent bloom.

The objective of the fungicide application is to cover as many petals as possible while ensuring that some chemical also penetrates into the canopy to help protect potential infection sites (such as leaf axils and bases). However, the fungicide is only active on petals present at the time of spraying and will not protect petals that emerge after spraying. Most fungicides are contact based with limited systemic function. Additionally, the curative abilities of most fungicides are limited on established sclerotinia stem rot lesions, especially those that are large or have penetrated stem tissue. Therefore it is important to apply the fungicide prior to significant petal drop, when environmental conditions are conducive to sclerotinia infection.

Registered fungicides are antagonistic and lethal to S. sclerotiorum ascospores and to newly-germinated hyphae, preventing the fungus from initiating the infection process. Canola flower petals which are not covered by fungicide may still initiate infection in crops that were sprayed. Since coverage of flower petals is a key consideration, the use of high water volumes is often recommended.

Research at Agriculture and Agri-Food Canada Saskatoon compared five methods of fungicide application over three years to determine the effect of nozzle type and pressure on sclerotinia stem rot infection of canola and crop yield. Variation in product performance among years indicated that environmental conditions had a major effect on crop development, sclerotinia stem rot infection, the effect of fungicides and subsequent yield. Overall, conventional flat fan nozzles (TeeJet XR), low-drift venturi nozzles (CFFC TurboDrop) and hollow cone nozzles (TeeJet TXVS-8) were all effective at reducing disease symptoms. Both 275 and 550 kilopascals (kPa), or 40 and 80 pounds per square inch (PSI) provided similar performance although increasing the venturi nozzle pressure to 550 kPa (80 PSI) improved disease control slightly. These results indicate that venturi nozzle technology is appropriate for use with foliar fungicides for sclerotinia control in canola provided pressures are adjusted to optimize nozzle performance8

Economics of fungicide application

sclerotinia risk assessment tool's economic calculator
The sclerotinia risk assessment tool’s economic calculator

The decision to apply a fungicide to prevent sclerotinia stem rot depends on the risk of the disease developing. Forecasting and risk analysis is discussed in detail in the section below. This decision may become clearer by answering these four questions:

  • Have environmental conditions prior to flowering been wet enough for apothecia development and survival?
  • Is the canola crop canopy dense and is yield potential high?
  • Does the weather forecast predict precipitation and/or humidity during the flowering period?
  • Is the pathogen present in sufficient quantities?

If the answer is “yes” to all four of these questions, then spraying is generally recommended. If the answer to some of the questions is “no”, then the decision is more difficult. Utilize the sclerotinia stem rot checklist to aid the decision, but also consider canola price and overall profit potential of the crop before investing more in it. Canola canopies with yield potential of less than 30 bushels per acre are less likely to suffer a sclerotinia stem rot infection big enough to make spraying economical, unless conditions for infection are ideal. Crops with an open canopy could be at lower risk, particularly if warm and windy weather allows them to dry out in the afternoons. However, if frequent rains and high humidity keep the plants wet, then there is still a threat. Rainfall at flowering and thick canola canopies increase the sclerotinia risk, especially if the field is located in an area where sclerotinia sprays are often warranted.

Canola Council of Canada research shows that it may be economically justifiable to apply fungicide when scouting indicates that disease incidence levels will reach 15 per cent in B. napus and over 30 per cent in B. rapa by crop maturity (no data on B. juncea is available). This is based on an $8 return per bushel ($353 per tonne) and an application cost of the fungicide at around $22 per acre ($55 per hectare).

As a rule of thumb, the potential yield loss in a field can be determined by:

Per cent potential yield loss =  Per cent disease incidence x 0.5
(where disease incidence = per cent of plants infected)

For example, a canola field with a 50 per cent of the plants infected with sclerotinia stem rot would have an approximate yield loss of 25 per cent (50 per cent disease incidence x 0.50 = 25 per cent). The actual yield losses depend on the environmental conditions, canopy structure, cultivar, and time of infection.

To calculate loss in revenue per acre, use the estimated per cent yield loss with the estimated yield of the field and the estimated market price for canola. If this lost revenue value is greater than the cost of a fungicide application per acre, then a fungicide application is recommended.

Revenue loss/acre =  Per cent potential yield loss  x  Estimated yield  x  cost per bushel

For example, consider a canola field with an estimated yield of 40 bushels per acre which is expected to sell for 10 dollars per acre. If the yield loss due to sclerotinia infection is 15 per cent, then the loss in revenue will be 60 dollars per acre. If the cost of fungicide application was 30 dollars per acre, then spraying a fungicide would have been economical (in this example).

Forecasting and risk assessment

There are a few different forecasting systems have been developed for predicting the risk of sclerotinia stem rot outbreaks in canola. While no forecast system is completely accurate, they do provide practical direction on making a decision as to whether a fungicide application is warranted. These tools may help a canola grower decide whether or not to spray fungicide, as long as the system used accounts for all the factors that will impact disease development.

Factors involved in forecasting

Many factors influence a forecasting system and its ability to predict the actual incidence of disease. Most predictive models evaluate several environmental and crop variables (in order of importance):

  • rainfall
  • soil moisture
  • weather forecast
  • canopy density and yield potential
  • cultivar resistance
  • ascospore presence
  • field disease history

Other variables that may affect the incidence of the disease include:

  • field cropping history
  • adjacent field disease history
  • changing ascospore levels during flowering
  • heat units
  • daily and weather related ascospore fluctuations
  • light penetration
  • leaf area index
  • crop height and lodging susceptibility
  • leaf wetness

Environmental conditions, in particular, the amount of available moisture leading up to and during flowering, has the largest impact on the development of sclerotinia stem rot in a field. The presence of the pathogen is normally expected to be present in most fields in Western Canada now that this fungus is so widely established and has so many hosts (including substantial canola acreage each year).

Sclerotinia stem rot checklist

Sclerotinia stem rot infection can vary greatly among fields and years, making scheduled routine spraying of fungicides unprofitable. However, when sclerotinia risk is high, preventative fungicide applications can effectively lower disease severity and improve yield. Assessment of disease risk within each field is essential to improve the odds that fungicides are only applied when it is economical to do so.

Determining whether or not the risk of sclerotinia warrants a fungicide application is a difficult decision. This decision depends on many variables including:

  • potential yield and price of the crop
  • cost of the fungicide
  • current and predicted rainfall
  • presence and level of ascospores
  • canola susceptibility

The Sclerotinia stem rot checklist is a comprehensive tool to assess the risk of sclerotinia stem rot developing in a given field. The checklist was first developed in Sweden, and has been modified for Canadian conditions. Growers should assess the crop and fill out the checklist for each field shortly after first flower (when 75 per cent of the canola plants have at least three open flowers). Usually this occurs during the last week of June or the first week of July. Read each question and add the point value assigned to the answer that best describes the conditions for that field. The total of the risk points from all questions represents the overall risk for sclerotinia. It is important to assess the risk early in the flowering period so that arrangements for chemical and application can be made if required. Continual monitoring up to full bloom is advisable as risk can change dramatically from early flower to full bloom.

The greater the score (total risk) for a field, the higher the probability of a positive economic return to a foliar fungicide application. Swedish researchers who developed this model (through evaluation of 800 fields over a 10-year period) found that fields with a total of less than 40 points, had a low risk of heavy infection (disease incidence exceeding 25 per cent). A threshold value of 40 risk points accurately identified 75 per cent of the fields that needed spraying for sclerotinia but also 16 per cent of the fields that did not need a fungicide. A threshold of 35 risk points increased the accuracy to almost 90 per cent of the fields that needed spraying but also included more than 20 per cent of the fields that did not need spraying. Therefore, they concluded that under their conditions if the risk points were 40 or higher, it was likely worth spraying. If the risk points were less than 40, it was not likely worth spraying. This provides a good guideline for use of the checklist in Canada, but growers should keep in mind that it may vary a bit under our field conditions, and also depending on fungicide cost and commodity price.

Measuring the pathogen

There are a few different methods to measure whether the pathogen S. sclerotiorum is likely present in a field. Petal tests, spore traps, and scouting for apothecia will all help to determine this factor for infection.

There are two types of petal tests currently available to determine if S. sclerotiorum is present on canola petals. One type of test uses DNA marker technology. Canola petals sampled from early flowers are sent to labs offering this service. The results are available in one to two days after the petals are received. The second type of petal test involves placing sampled petals on specifically produced selective agar-plates to observe if S. sclerotiorum mycelium grows from these petals. This test can be done by canola grower or agronomists, but it takes about a week before results are available.

sclerotinia risk assessment tool's resources
The sclerotinia risk assessment tool resources, including a sclerotinia rating method video, photos and and sclerotia depot content to support sclerotinia management efforts.

Spore trapping samplers can be installed in a canola field, which will capture the wind-blown S. sclerotiorum ascospores on a media or cassette. These spore-trapped samples are sent to a testing lab, which will provide results in one or two days after the samples are received.

Scouting for apothecia is an indirect method to determine if ascospores may be present and infecting canola flower petals. Apothecia are tan or honey-coloured, five to 15 millimetres across, and have tops which are cupped like a golf tee. They will be growing from sclerotia in the soil or decaying canola. There are other fungal structures or mushrooms produced by saprophytic fungi, meaning that they survive on decaying crop residue that can occur in similar conditions but are not apothecia. The spores produced from these fungi do not contribute to increased sclerotinia risk. Above the soil surface the stalks of apothecia tend to be short, so mushrooms with stalks that extend above the soil surface (e.g. 25 millimetres or more) are unlikely to be apothecia of sclerotinia. Mushrooms with rounded tops or bright colours are not likely apothecia of the sclerotinia fungus. Apothecia may be found in a canola field, but they are often likely observed in adjacent fields that had canola or some other susceptible crop (such as sunflowers, soybeans, lentils, etc.) in the previous year.

All of these pathogen measurement tools only help determine one factor in forecasting this disease: ascospore presence. Environmental conditions still need to be considered before one decides to apply a fungicide. Using pathogen measurement results along with the Sclerotinia stem rot checklist is recommended.

Modelling the weather

Rainfall and soil moisture are necessary for sclerotia germination, spore production, and spore germination and growth. Ideal canola growing weather is also ideal for sclerotinia. Soil moisture indicates sclerotia germination and, therefore, the potential for ascospore production rather than infection and disease development. Frequently water from heavy dews dripping off the plant is enough moisture for sclerotia germination.

Weather forecasts can improve the reliability of the disease forecast because sudden weather changes can cause infestations to occur unexpectedly or high risk fields may show limited disease development. Hot, dry weather can greatly reduce the risk of sclerotinia infection.

Commercial weather measuring services offer sclerotinia forecasts based on local environmental conditions recorded at the field level. These highly specific measurements provide a comprehensive data set to help make a fungicide application decision. However none of the weather models have been validated for their accuracy in Western Canada, so far. Canola growers should be aware that these may not be providing the right forecast at this point in time. Weather prediction models do not provide a measurement of pathogen presence, so pathogen sampling may still be required. Combining weather prediction with the Sclerotinia stem rot checklist is recommended.

Field history

Field and nearby field cropping and disease history are an indirect average of measuring the potential for presence of ascospores. While apothecia produced from sclerotia within the field are considered the main source of spores, spores produced in nearby fields and blown into the crop are important in disease development. Research has shown that most ascospores are deposited within 100 meters of the source, and therefore adjacent fields can be an important source of inoculum. Fields with sclerotia at distances of greater than 500 metres to two kilometres would likely represent a minimal source of inoculum, as most ascospores would have been deposited within 100 to 400 metres of the apothecia from which they were produced9,10,11.

Crop canopy density

Crop canopy density can influence the risk of sclerotinia, given favourable environmental conditions12. The crop canopy can be modified by seeding rate, row spacing and fertility, which is the main factor impacting crop canopy density. Generally a high population of rapidly growing plants leads to faster canopy closure and thick, dense canopies. While these dense canopies often have the greatest yield potential, they tend to maintain high soil moisture levels beneath the canopy, increasing the germination of sclerotia. Moist soil conditions for approximately 10 days or more induces sclerotia to form apothecia and subsequent spore release. Moist conditions in the lower canopy also increase the chances of infection being initiated when petals carrying spores land on lower leaves or leaf axils. In short season growing areas, B. rapa varieties tend to have lighter canopies and generally lower infection levels.

Cultivar selection

There are currently canola cultivars on the market in Canada with sclerotinia resistance or tolerance. These cultivars have demonstrated reduced levels of sclerotinia stem rot infection in field and laboratory trials. The mechanisms for this increased level of tolerance or resistance are not well described, but they do appear to reduce lesion development in stem and other tissues. This reduced severity of sclerotinia stem rot is effective but may not match the same level of control as a fungicide application. Therefore under high risk of disease development a fungicide application to these cultivars may still be necessary.

To determine the amount of resistance or tolerance a cultivar has to sclerotinia stem rot, the canola industry has agreed to use the protocol developed by Dr. Lone Buchwaldt (from Agriculture and Agri-Food Canada) and the Pathology sub-committee of the Western Canada Canola/Rapeseed Recommending Committee. This protocol outlines the steps necessary in order to correctly test for sclerotinia resistance and to correctly label the amount of resistance for cultivar descriptions and marketing purposes. Additionally some seed developers may use their own sclerotinia stem rot rating system to describe the reduction in sclerotinia stem rot infection, which may incorporate architectural and canopy structural components which may reduce infection.

Sclerotinia stem rot has been observed to be severe in heavily lodged fields or areas within a field. Therefore choosing cultivars that resist lodging may reduce sclerotinia severity.

Biological controls

Currently there are two biological products available for sclerotinia stem rot control in Canada: Contans and Serenade OPTI. Contans is a biological control product registered for control in canola as well as soybeans, dry edible beans, sunflower and safflower. The active ingredient is Coniothyrium minitans, a fungus that colonizes and slowly degrades the sclerotia when it comes in contact. The product is a pre-emergent bio-fungicide that requires several months for the fungus to destroy the viability of the sclerotia.

Serenade OPTI is a bacterial formulation of Bacillus subtillis which is applied in a foliar fashion at the 20 to 30 per cent bloom stage of canola, similar to how fungicides are applied. B. subtillis is antagonistic to fragile ascospores and newly developing hyphae.

Cultural controls

There are a number of agronomic or cultural considerations to examine with sclerotinia stem rot.

Crop rotation

Crop rotation is not always effective for managing sclerotinia stem rot because S. sclerotiorum can be host on many plants (including many popular crops in Western Canada) and because the fungus has the  ability to survive for years in the soil as sclerotia. Also, air-borne ascospores can blow in from nearby fields, where they are released by apothecia germinating from sclerotia left from previous broadleaf crops. Regardless, the opportunity for high sclerotinia stem rot disease levels is maximized if broadleaf crops are grown consecutively due to increased potential for spore production within the field.

Cereals and grasses are not susceptible, and can help reduce viable sclerotia in the soil through decay and germination in the absence of susceptible hosts. Therefore, it is better to avoid seeding canola adjacent to a field that had a heavily infected crop the previous year. Control of susceptible weeds and volunteer plants in cereal crops also helps to avoid replenishing viable sclerotia levels.


Use of clean pedigreed seed, free of sclerotia is recommended. Since crop density is an important factor, avoid exceeding the recommended seeding rate. Research at the University of Manitoba found that increasing seeding rates two or three times above normal seeding rates can lead to lodging, which can increase sclerotinia infection13. Lighter seeding rates or wider row spacing may increase ventilation within the crop canopy and reduce the moist soil microclimate required for sclerotia to germinate, helping to reduce sclerotinia levels. However, seeding rates need to be adequate to produce a minimum of five to eight viable plants per square foot or yields may be compromised regardless of sclerotinia levels. Also, frequent rainfall and/or persistently high humidity may create a suitable environment for infection in spite of an open canopy.

Harvest and grade

Growers can apply fungicide for sclerotinia stem rot control and achieve good to excellent results in the standing crop. Unfortunately, this disease may progress rapidly in the swath in wet years particularly in B. napus cultivars. Do not swath canola crops with significant incidence of infection if rain is forecast, particularly if the crop is immature (green) when cut. In wet compacted swaths, particularly on the turns, sclerotinia rot can progress rapidly. The disease can be detected by a rotten egg-like smell coming from the swaths. This problem is obviously more prevalent in the wetter regions of Western Canada. The heavier and more compact the swath, the greater the likelihood for sclerotinia to rot the swath before combining.

Steps to follow to control sclerotinia in the swath:

  • Do not swath immature stands (target greater than 60 per cent seed colour change among the healthy plants).
  • Do not swath if rain is in the immediate forecast.
  • Avoid compacting swaths.
  • Use a high cut to allow for better drying.
  • Avoid heavy swaths on the turns.
  • Consider straight combining the crop, but recognize that shattering losses from prematurely ripened infected plants will be significant if a pod shatter cultivar is not grown.

Up to one-third of a canola crop may be lost in the swath due to sclerotinia stem rot. Additionally, this increases the number of sclerotia which may be left in a field after harvest.

It may also result in the downgrading of canola due to sclerotia in the seed sample. Tolerances for sclerotia are very low. Seeds Regulations, which applies to mustard and canola, has a separate standard for the number sclerotia bodies allowed for each grade. When performing a purity analysis on the crop, sclerotia bodies are reported per 50 grams (Table VII with SCHEDULE I of the Seeds Regulation).

Table 2. Canola grade quality factor

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